IMPORTANT: software configuration optimized and better modularized

Summary: after merging this commit into your project, it should be
re-configured since the location of software installation files like
'LOCAL.conf' or the LaTeX macros of the software environment have
changed. But it should not affect the analysis phase of your project.

Until this commit, it was not possible to run a pre-built Maneage'd project
(in a container) on a newly cloned Maneage'd project source. This was
because the containers should be read-only, but during the various checks
of the configuration (to verify that we are using the same software
environment in the container and the source), we were writing/testing many
things in the build directory, and 'LOCAL.conf' which was actually in the
source directory!

Furthermore, the '.local' and '.build' were built at configure time, making
it hard to run the same container from a newly cloned Maneage'd project. To
make things harder for the scenario above, the 'configure.sh' script would
pause on every message and didn't have a quiet mode (making it practically
impossible to run './project configure' before './project make' on every
container run).

With this commit, all these issues have been addressed and it is now
possible to simply get a built container, clone a Maneage'd project and run
the analysis (using the built environment of the container that is verified
on every run). The respective changes/additions are described below:

 - The high-level container scripts ('apptainer.sh' and 'docker.sh', along
   with their READMEs) have been moved to the 'reproduce/software/shell'
   directory and the old 'reproduce/software/containers' directory has been
   deleted. This is because we have classified the software files by their
   language/format and the container scripts are scripts in the end.

 - The './project' script:

    - Now has two extra options: '--quiet' and '--no-pause'. Both are
      directly passed to the 'configure.sh' script. They will respectively
      disable any informative printed message or any pause after that
      message (if it is printed).

    - The '--build-dir' option is now also relevant for './project make':
      when it is given, it will re-create the two '.build' and '.local'
      symbolic links at the top source directory in all scenarios
      ('configure', 'make' or 'shell'). This will allow both the
      configuration, analysis and shell phases to safely assume they exist
      and match the user's desire at run-time.

    - The build/analysis directory's sub-directories that need to be built
      before 'top-make.mk' are now built in a separate function to help in
      readability.

 - The 'configure.sh' script:

    - For developers: a new 'check_elapsed' variable has been defined that
      will enable the newly added 'elapsed_time_from_prev_step'
      function. This function should be used from now on at the end of
      every major step to help find bottlenecks.

 - The targets of the software in 'pre-make-build.sh' now also have the
   version of the software in their file name. Until now, they didn't have
   the version, so there was no way to detect if the software has been
   updated or not in the source. For Lzip and Make (that also get built
   after GCC), the ones in this script have a '-pre-make' suffix also.

 - 'Local.conf.in' now has descriptions for every variable.

 - The '-std=gnu17' option is now used instead of '-std=c17' for basic
   software that cannot be built without specifying the C standard in GCC
   15.1 (described in previous commit: 2881fc0a6205). See [1] for more
   details; in summary: '-std=gnu17' is also supported on macOS's Clang and
   has some features that 'pkg-config' needs

 - Generally: some longer code lines have been broken or indentation
   decreased to fit the 75 character line length. This has not reduced
   readability however. For example the long 'echo' commands are now
   replaced by multiple 'printf's, or the indentation is still clearly
   visible.

The seeds of the work on this commit started by a branch containing three
commits by Giacomo Lorenzetti (133 insertions, 100 deletions). Upon merging
with the main 'maneage' branch, they were generalized and re-organized to
become this commit.

The following issues have also been addressed with this commit:

 - The LaTeX calls (during the building of 'paper.pdf') do not contain
   Maneage'd dynamic libraries. This is because we don't build the LaTeX
   binaries from source, an TeXLive manager uses the host environment.

 - The 'docker.sh' script:

    - Adds the '--project-name' option: its internal variable existed, but
      the option for the user to define it at run-time was not.

    - Ported to macOS: it does not check being a member of the 'docker'
      group, and finds the number of threads using macOS-specific tools.

 - The 'apptainer.sh' script:

    - Now installs 'wget' in the base container also (necessary when the
      user doesn't have the tarballs).

[1] https://savannah.nongnu.org/bugs/?67068#comment2

2 files changed, 15 insertions, 12 deletions

diff --git a/reproduce/software/make/basic.mk b/reproduce/software/make/basic.mk
index c9aba96..4b18c29 100644
--- a/reproduce/software/make/basic.mk
+++ b/reproduce/software/make/basic.mk
@@ -39,7 +39,7 @@
 # along with this Makefile.  If not, see <http://www.gnu.org/licenses/>.
 
 # Top level environment
-include reproduce/software/config/LOCAL.conf
+include .build/software/config/LOCAL.conf
 include reproduce/software/make/build-rules.mk
 include reproduce/software/config/versions.conf
 include reproduce/software/config/checksums.conf
@@ -63,10 +63,13 @@ ibidir   = $(BDIR)/software/installed/version-info/proglib
 # editor) is installed by default, it is recommended to have it in the
 # 'basic.mk', so Maneaged projects can be edited on any system (even when
 # there is no command-line text editor available).
+#
+# The recipe is '@echo > /dev/null' so Make does not print "make: Nothing
+# to be done for 'all'."
 targets-proglib = low-level-links \
                   gcc-$(gcc-version) \
                   nano-$(nano-version)
-all: $(foreach p, $(targets-proglib), $(ibidir)/$(p))
+all: $(foreach p, $(targets-proglib), $(ibidir)/$(p)); @echo > /dev/null
 
 # Define the shell environment
 # ----------------------------
@@ -423,7 +426,7 @@ $(ibidir)/ncurses-$(ncurses-version): $(ibidir)/patchelf-$(patchelf-version)
 	rm -f $(ibdir)/bash* $(ibdir)/awk* $(ibdir)/gawk*
 
 #	Standard build process.
-	export CFLAGS="-std=c17 $$CFLAGS"
+	export CFLAGS="-std=gnu17 $$CFLAGS"
 	$(call gbuild, ncurses-$(ncurses-version), static, \
 	               --with-shared --enable-rpath --without-normal \
 	               --without-debug --with-cxx-binding \
@@ -562,7 +565,7 @@ $(ibidir)/bash-$(bash-version): \
 	if [ "x$(static_build)" = xyes ]; then stopt="--enable-static-link"
 	else                                   stopt=""
 	fi;
-	export CFLAGS="$$CFLAGS -std=c17 \
+	export CFLAGS="$$CFLAGS -std=gnu17 \
 	               -DDEFAULT_PATH_VALUE='\"$(ibdir)\"' \
 	               -DSTANDARD_UTILS_PATH='\"$(ibdir)\"'  \
 	               -DSYS_BASHRC='\"$(BASH_ENV)\"' "
@@ -1015,7 +1018,7 @@ $(ibidir)/gmp-$(gmp-version): \
               $(ibidir)/coreutils-$(coreutils-version)
 	tarball=gmp-$(gmp-version).tar.lz
 	$(call import-source, $(gmp-url), $(gmp-checksum))
-	export CFLAGS="-std=c17 $$CFLAGS"
+	export CFLAGS="-std=gnu17 $$CFLAGS"
 	$(call gbuild, gmp-$(gmp-version), static, \
 	               --enable-cxx --enable-fat, \
 	               -j$(numthreads))
@@ -1076,7 +1079,7 @@ $(ibidir)/grep-$(grep-version): $(ibidir)/coreutils-$(coreutils-version)
 $(ibidir)/m4-$(m4-version): $(ibidir)/patchelf-$(patchelf-version)
 	tarball=m4-$(m4-version).tar.lz
 	$(call import-source, $(m4-url), $(m4-checksum))
-	export CFLAGS="-std=c17 $$CFLAGS"
+	export CFLAGS="-std=gnu17 $$CFLAGS"
 	$(call gbuild, m4-$(m4-version), static, \
 	               --with-syscmd-shell=$(ibdir)/dash, \
 	               -j$(numthreads) V=1)
@@ -1109,7 +1112,7 @@ $(ibidir)/pkg-config-$(pkgconfig-version): $(ibidir)/patchelf-$(patchelf-version
 	if [ x$(on_mac_os) = xyes ]; then export compiler="CC=clang"
 	else                              export compiler=""
 	fi
-	export CFLAGS="-std=c17 $$CFLAGS"
+	export CFLAGS="-std=gnu17 $$CFLAGS"
 	$(call gbuild, pkg-config-$(pkgconfig-version), static, \
 	               $$compiler --with-internal-glib \
 	               --with-pc-path=$(ildir)/pkgconfig, V=1)
diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk
index 4ed5d62..67ca8b6 100644
--- a/reproduce/software/make/high-level.mk
+++ b/reproduce/software/make/high-level.mk
@@ -29,7 +29,7 @@
 # along with this Makefile.  If not, see <http://www.gnu.org/licenses/>.
 
 # Top level environment (same as 'basic.mk')
-include reproduce/software/config/LOCAL.conf
+include .build/software/config/LOCAL.conf
 include reproduce/software/make/build-rules.mk
 include reproduce/software/config/versions.conf
 include reproduce/software/config/checksums.conf
@@ -123,11 +123,12 @@ ifneq ($(strip $(offline)),1)
   target-texlive := $(itidir)/texlive
 endif
 
-# Ultimate Makefile target.
+# Ultimate Makefile target. The recipe is '@echo > /dev/null' so Make does
+# not print "make: Nothing to be done for 'all'."
 all: $(foreach p, $(targets-proglib), $(ibidir)/$(p)) \
      $(foreach p, $(targets-python), $(ipydir)/$(p)) \
      $(foreach p, $(targets-r-cran),  $(ircrandir)/$(p)) \
-     $(target-texlive)
+     $(target-texlive); @echo > /dev/null
 
 # Define the shell environment
 # ----------------------------
@@ -2020,7 +2021,7 @@ $(itidir)/texlive: reproduce/software/config/texlive-packages.conf \
 #	  We do not build TeXLive from source and for its installation it
 #	  downloads components from the web internally; and those
 #	  components can use '/bin/sh' (which needs 'sys_library_sh_path').
-	  export LD_LIBRARY_PATH="$(sys_library_sh_path):$$LD_LIBRARY_PATH"
+	  export LD_LIBRARY_PATH="$(sys_library_sh_path)"
 
 #	  To update itself, tlmgr needs a backup directory.
 	  backupdir=$(idir)/texlive/backups
@@ -2049,7 +2050,6 @@ $(itidir)/texlive: reproduce/software/config/texlive-packages.conf \
 #	  files (this is because we do no yet install LaTeX from source):
 	  cdir=$$(pwd)
 	  cd $(idir)/texlive
-	  $(shsrcdir)/prep-source.sh $(ibdir)
 	  cd $$cdir
 
 #	  Get all the necessary versions.